I've added five additional #709 sequences to the existing alignment file, and posted the final alignment file and tree.

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I believe some groups are still in the process of reverse complementing inserts in the non-usual orientation.

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A student who is recovering from illness may also post a few additional #712 sequences and an updated alignment and tree file this weekend. She will not delete the old file, since many of you are already using it, but will simply add hers as another option to use in your reports.

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Agi is in the process of trimming and analyzing four additional #709 clones prepped and sequenced yesterday -- looks as though only one will be good. I may not finish until after class today, circa 5 pm. Update: even later than that. I can do the final addition to an existing #709 .mas file if need be, also including samples from a student who has been ill.

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Consider doing a "watch" on this page so you know when it changes.

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I'd also like to link my Excel species worksheet [[Media: S13-M1D7-709-extra-clones.xlsx | right here]]. You can see that I had a few interesting decisions to make, which perhaps could apply to some of you as well. I don't expect any more changes to the trees at this point, but perhaps for the revision you can revisit your choices. More specifically: (1) in some cases I had only partial sequence, so I made naming decisions at a higher taxonomic level; (2) in one case the top choice was misleading because it was a partial sequence; (3) One sequence was longer than usual, which took a bit of extra searching to process during the trimming stage, because there was so little sequence overlap.

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[[User:AgiStachowiak|AgiStachowiak]] 16:19, 8 March 2013 (EST)

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An updated version of the #739 alignment file & tree was posted to get rid of duplicates of some insert sequences.

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[[User:Sarah N. Yu|Sarah N. Yu]] 21:13, 8 March 2013 (EST)

==Final sample-wide alignment files and trees==

==Final sample-wide alignment files and trees==

One representative from each sample-based group should post a .mas and .pdf file here when data are in final form. That way we'll all have quick access to the location sub-trees.

One representative from each sample-based group should post a .mas and .pdf file here when data are in final form. That way we'll all have quick access to the location sub-trees.

Current revision

Contents

General notes and updates

I've added five additional #709 sequences to the existing alignment file, and posted the final alignment file and tree.

A student who is recovering from illness may also post a few additional #712 sequences and an updated alignment and tree file this weekend. She will not delete the old file, since many of you are already using it, but will simply add hers as another option to use in your reports.

Consider doing a "watch" on this page so you know when it changes.

I'd also like to link my Excel species worksheet right here. You can see that I had a few interesting decisions to make, which perhaps could apply to some of you as well. I don't expect any more changes to the trees at this point, but perhaps for the revision you can revisit your choices. More specifically: (1) in some cases I had only partial sequence, so I made naming decisions at a higher taxonomic level; (2) in one case the top choice was misleading because it was a partial sequence; (3) One sequence was longer than usual, which took a bit of extra searching to process during the trimming stage, because there was so little sequence overlap.